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h.draisma
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@hdraisma-15174
Last seen 6.7 years ago
Trying to run the examples as in the "Examples" section on the coMET() help page reproducibly returns the following error:
Error in genesENSEMBL(gen, chrom, start, end, showId = TRUE): could not find function "genesENSEMBL"
By "reproducibly" I mean that the same error was returned before and after removing the 'coMET' package from my <R> installation and reinstalling then loading it, allowing "all" dependencies (packages) to be updated when prompted.
The sequence of commands that I followed in <R> for this was:
> require(coMET)
> example(coMET)
> remove.packages("coMET", lib="~/R/x86_64-pc-linux-gnu-library/3.4")
> require(coMET) #<-- Apparently allowed me to load the package still indeed, hence closed <R>, then restarted <R>. After that, issuing the same command produced an error stating that the package 'coMET' was not available indeed, as we want.
> source("https://bioconductor.org/biocLite.R")
> biocLite("coMET")
> require(coMET)
> example("coMET")
The outputs of '> example("coMET", verbose = TRUE)', "> sessionInfo()" and "> traceback()" are as follows:
> example("coMET", verbose = TRUE)
'envir' chosen:<environment: R_GlobalEnv>
encoding = "UTF-8" chosen
--> parsed 10 expressions; now eval(.)ing them:
has srcrefs:
List of 10
$ :Class 'srcref' atomic [1:8] 10 1 10 64 1 64 10 10
.. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref' atomic [1:8] 11 1 11 65 1 65 11 11
.. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref' atomic [1:8] 12 1 12 55 1 55 12 12
.. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref' atomic [1:8] 13 1 13 74 1 74 13 13
.. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref' atomic [1:8] 14 1 14 65 1 65 14 14
.. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref' atomic [1:8] 16 1 16 15 1 15 16 16
.. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref' atomic [1:8] 17 1 17 17 1 17 17 17
.. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref' atomic [1:8] 18 1 18 15 1 15 18 18
.. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref' atomic [1:8] 19 1 19 13 1 13 19 19
.. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref' atomic [1:8] 21 1 57 1 1 1 21 57
.. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
>>>> eval(expression_nr. 1 )
=================
coMET> extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
curr.fun: symbol <-
.. after 'expression(extdata <- system.file("extdata", package="coMET",mustWork=TRUE))'
>>>> eval(expression_nr. 2 )
=================
coMET> configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt")
curr.fun: symbol <-
.. after 'expression(configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt"))'
>>>> eval(expression_nr. 3 )
=================
coMET> myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
curr.fun: symbol <-
.. after 'expression(myinfofile <- file.path(extdata, "cyp1b1_infofile.txt"))'
>>>> eval(expression_nr. 4 )
=================
coMET> myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
curr.fun: symbol <-
.. after 'expression(myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt"))'
>>>> eval(expression_nr. 5 )
=================
coMET> mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
curr.fun: symbol <-
.. after 'expression(mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt"))'
>>>> eval(expression_nr. 6 )
=================
coMET> chrom <- "chr2"
curr.fun: symbol <-
.. after 'expression(chrom <- "chr2")'
>>>> eval(expression_nr. 7 )
=================
coMET> start <- 38290160
curr.fun: symbol <-
.. after 'expression(start <- 38290160)'
>>>> eval(expression_nr. 8 )
=================
coMET> end <- 38303219
curr.fun: symbol <-
.. after 'expression(end <- 38303219)'
>>>> eval(expression_nr. 9 )
=================
coMET> gen <- "hg38"
curr.fun: symbol <-
.. after 'expression(gen <- "hg38")'
>>>> eval(expression_nr. 10 )
=================
coMET> if(interactive()){
coMET+ genetrack <-genesENSEMBL(gen,chrom,start,end,showId=TRUE)
coMET+ snptrack <- snpBiomart(chrom, start, end,
coMET+ dataset="hsapiens_snp_som",showId=FALSE)
coMET+ strutrack <- structureBiomart(chrom, start, end,
coMET+ strand, dataset="hsapiens_structvar_som")
coMET+ clinVariant<-ClinVarMainTrack(gen,chrom,start,end)
coMET+ clinCNV<-ClinVarCnvTrack(gen,chrom,start,end)
coMET+ gwastrack <-GWASTrack(gen,chrom,start,end)
coMET+ geneRtrack <-GeneReviewsTrack(gen,chrom,start,end)
coMET+
coMET+ listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
coMET+ clinCNV,gwastrack,geneRtrack)
coMET+
coMET+ comet(config.file=configfile, mydata.file=myinfofile, mydata.type="listfile",
coMET+ cormatrix.file=mycorrelation, cormatrix.type="listfile",
coMET+ mydata.file=myexpressfile, mydata.large.type="listfile",
coMET+ tracks.gviz=listgviz,
coMET+ verbose=FALSE, print.image=FALSE,disp.pvalueplot=TRUE)
coMET+ } else {
coMET+ data(geneENSEMBLtrack)
coMET+ data(snpBiomarttrack)
coMET+ data(ISCAtrack)
coMET+ data(strucBiomarttrack)
coMET+ data(ClinVarCnvTrack)
coMET+ data(clinVarMaintrack)
coMET+ data(GWASTrack)
coMET+ data(GeneReviewTrack)
coMET+
coMET+ listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
coMET+ clinCNV,gwastrack,geneRtrack)
coMET+ comet(config.file=configfile, mydata.file=myinfofile, mydata.type="listfile",
coMET+ cormatrix.file=mycorrelation, cormatrix.type="listfile",
coMET+ mydata.large.file=myexpressfile, mydata.large.type="listfile",
coMET+ tracks.gviz=listgviz,
coMET+ verbose=FALSE, print.image=FALSE,disp.pvalueplot=TRUE)
coMET+ }
Error in genesENSEMBL(gen, chrom, start, end, showId = TRUE) :
could not find function "genesENSEMBL"
> traceback()
5: eval(ei, envir)
4: eval(ei, envir)
3: withVisible(eval(ei, envir))
2: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix,
getOption("prompt")), continue.echo = paste0(prompt.prefix,
getOption("continue")), verbose = verbose, max.deparse.length = Inf,
encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
1: example("coMET", verbose = TRUE)
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 grid stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] coMET_1.10.2 trackViewer_1.14.1 ggbio_1.26.0
[4] ggplot2_2.2.1 psych_1.7.8 Gviz_1.22.3
[7] GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 IRanges_2.12.0
[10] S4Vectors_0.16.0 BiocGenerics_0.24.0 biomaRt_2.34.2
[13] BiocInstaller_1.28.0
loaded via a namespace (and not attached):
[1] nlme_3.1-131 ProtGenerics_1.10.0
[3] bitops_1.0-6 matrixStats_0.53.1
[5] bit64_0.9-7 RColorBrewer_1.1-2
[7] progress_1.1.2 httr_1.3.1
[9] tools_3.4.3 backports_1.1.2
[11] R6_2.2.2 rpart_4.1-13
[13] Hmisc_4.1-1 DBI_0.8
[15] lazyeval_0.2.1 colorspace_1.3-2
[17] nnet_7.3-12 gridExtra_2.3
[19] prettyunits_1.0.2 GGally_1.3.2
[21] mnormt_1.5-5 RMySQL_0.10.14
[23] bit_1.1-12 curl_3.1
[25] compiler_3.4.3 graph_1.56.0
[27] Biobase_2.38.0 htmlTable_1.11.2
[29] grImport_0.9-0 DelayedArray_0.4.1
[31] rtracklayer_1.38.3 scales_0.5.0
[33] checkmate_1.8.5 pbapply_1.3-4
[35] RBGL_1.54.0 stringr_1.3.0
[37] digest_0.6.15 Rsamtools_1.30.0
[39] foreign_0.8-69 XVector_0.18.0
[41] base64enc_0.1-3 dichromat_2.0-0
[43] htmltools_0.3.6 ensembldb_2.2.2
[45] BSgenome_1.46.0 htmlwidgets_1.0
[47] rlang_0.2.0 rstudioapi_0.7
[49] RSQLite_2.0 shiny_1.0.5
[51] BiocParallel_1.12.0 acepack_1.4.1
[53] VariantAnnotation_1.24.5 RCurl_1.95-4.10
[55] magrittr_1.5 GenomeInfoDbData_1.0.0
[57] Formula_1.2-2 Matrix_1.2-11
[59] Rcpp_0.12.15 munsell_0.4.3
[61] stringi_1.1.6 yaml_2.1.17
[63] SummarizedExperiment_1.8.1 zlibbioc_1.24.0
[65] plyr_1.8.4 AnnotationHub_2.10.1
[67] blob_1.1.0 lattice_0.20-35
[69] Biostrings_2.46.0 splines_3.4.3
[71] hash_2.2.6 GenomicFeatures_1.30.3
[73] knitr_1.20 pillar_1.2.1
[75] reshape2_1.4.3 XML_3.98-1.10
[77] biovizBase_1.26.0 latticeExtra_0.6-28
[79] data.table_1.10.4-3 httpuv_1.3.6.2
[81] gtable_0.2.0 reshape_0.8.7
[83] assertthat_0.2.0 mime_0.5
[85] xtable_1.8-2 AnnotationFilter_1.2.0
[87] colortools_0.1.5 survival_2.41-3
[89] OrganismDbi_1.20.0 tibble_1.4.2
[91] GenomicAlignments_1.14.1 AnnotationDbi_1.40.0
[93] memoise_1.1.0 corrplot_0.84
[95] cluster_2.0.6 interactiveDisplayBase_1.16.0
>
